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Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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read structure populated from runParameters.xml #2

Closed Kurt-Hetrick closed 1 year ago

Kurt-Hetrick commented 2 years ago

as far as I can tell, it should be possible and removes a field that I am not sure how the end user would know otherwise.

e.g. a run structure of

47T8B9M1S8B47T

should be be determined from this in the xml file...i think...might have to look into this a little more...

\47</Read1NumberOfCycles> \47</Read2NumberOfCycles> \18</IndexRead1NumberOfCycles> \8</IndexRead2NumberOfCycles>

Kurt-Hetrick commented 1 year ago

after talking to Brian, I should check that the runparamters.xml has expected values, if not, then populate read structure with a value that he had to use for peters.

Kurt-Hetrick commented 1 year ago

this file is not equipped to actually determine how the read structure was performed. you would have to rely on assumptions. a possibility it to parse the file and make an assumption by default and if the assumption is not valid give the end user the option to change it when submitting it. but that is another issue. so i'm closing this one and leaving the other one open for the lab managers to tell me which they would rather try first. currently leaving read structure as a required option on submission.